Questions tagged [cheminformatics]

Cheminformatics involves the production, processing, filtering, and searching of chemical information. This includes chemical databases, computational screening, searching, etc.

Filter by
Sorted by
Tagged with
22
votes
1answer
551 views

Structure that breaks InChI

I am currently testing a piece of software that generates the InChI for a given structure. I also want to test error situations as end users will also deliver the mol files that will be used as input ...
17
votes
4answers
1k views

Is there a formula to tell how many conformers of a molecule to generate?

Let's say we want to generate conformers of molecules (e.g., ligands for docking in a protein pocket). Is there a formula, like a function of the number of rotatable bonds, to decide how many ...
14
votes
3answers
2k views

Pubchem, InChI, SMILES, and uniqueness

PubChem compound 6140 is L-phenylalanine in its neutral (not zwitterionic) form. According this PubChem, this molecule has the following SMILES and InChI indentifiers: SMILES: C1=CC=C(C=C1)CC(C(=O)O)...
14
votes
2answers
858 views

How should elements be colored? And how many bonds does an atom have?

I'm working on my own 3D molecule viewer for my AP Chem class. So far everything's going together nicely. There's a couple of things I'm not sure about though... Is there a certain rule of thumb or ...
14
votes
2answers
2k views

How do I make 3d molecular graphics similar to those shown on Wikipedia?

I want to make 3d molecular graphics similar to those found on Wikipedia. In the page for benzene, you can see the structure looks like this: However, if I go to the interactive image as shown in ...
14
votes
3answers
2k views

Portable library to render 2D structural formulas as vector graphics from SMILES or InChI

For a web-based project, I am looking for a piece of software to create a 2D vector graphics structural formula from a textual structure encoding scheme such as SMILES or InChI, running on the server ...
14
votes
2answers
559 views

How do I create a spreadsheet containing the coordinates and predicted bond angles, molecular properties, torsion properties, etc of a molecule?

On a previous answer here (https://chemistry.stackexchange.com/a/30841/876) I was informed in the comments that OpenBabel & Python terminal could be used to print the data contained in the ...
12
votes
5answers
10k views

Is there a way to use free software to convert SMILES strings to structures?

So far I've been unsuccessful in finding an open source tool that will convert a large number (>100k) of SMILES strings to a chemical structure. Is this really only solved by commercial applications? ...
12
votes
3answers
941 views

What are datasets containing molecules with more than 38 heavy atoms?

I have been testing a machine learning approach for molecular energy prediction. The current dataset that I have is QM9, which is consist of molecules with up to 9 heavy atoms. I was wondering if ...
12
votes
4answers
2k views

Public API for physical properties

Is there a publicly available API that serves physical property data for organic molecules? Pubchem does not serve properties, ChemSpider closes property access to API calls, and Toxnet only serves ...
11
votes
6answers
14k views

How many unique molecules exist? And how many exist only by synthesis? [closed]

I'm interested in How many unique molecules (of all types: organic and inorganic, etc), exist in the world accessible by man (let's exclude black holes and the centers of stars etc)? What subset ...
11
votes
3answers
980 views

List of functional groups in a molecule

Does anyone know if there's a tool for listing the functional groups present in a molecule?
11
votes
3answers
2k views

Is converting SMARTS to SMILES a “lossless” operation?

The following three different SMARTS strings represent the same structure - at least when depicting it (e.g. at Uni Hamburg Smarts viewer). ...
11
votes
1answer
347 views

Trying to understand SMILES(?) patterns

In the example calculation from the conformer search package fafoom is a mysterious pattern that I'd like to understand. The SMILES code of the given example structure is: ...
10
votes
3answers
434 views

How does a molecule search work by drawing in visual editor?

There are a lot of chemical search engines (such as ChemSpider's Structure search) that allow users to draw and search for a molecule. How does it work? Is the comparison of images used? Could you ...
10
votes
1answer
586 views

What would be SMILES notation for a compound with delocalized bonding?

For example, the cyclopentadienyl rings in ferrocene $\ce{Fe(}\eta^5 \ce{-C5H5)2}$ are often drawn with delocalized electron circles in them instead of explicit pi bonds. The Wikipedia article for ...
9
votes
3answers
1k views

InChIKey generation from InChI

I am trying to find some good resources to understand generation of InChIKeys from the InChI. There seems to be no resource available online. I have gone through the Wikipedia article for InChI, but ...
9
votes
1answer
721 views

How to get the SMILES of all compounds on PubChem?

I would like to download all the compounds from ChEMBL and PubChem. For ChEMBL this is easy using their webUI. Nevertheless, for PubChem, it isn't clear how to download all the compounds on the ...
9
votes
2answers
453 views

Any program for conformational searching for sugars?

I want to estimate mean Gibbs free energy of formation of glucose and for that purpose I think conformers of ring flip should be taken into account. Do you know if some free program can find those ...
8
votes
1answer
355 views

Is it possible to build or embed the SMILES representation of compounds in 3D?

I would like to know if there is a proper way to get the 3D information from the SMILES string of a molecule. Is there a standard way to embed a SMILES string in 3D space? Are there other ...
8
votes
1answer
224 views

How to determine the correct InChI for a certain compound?

Let's say I have a compound L-xylulose 1-phosphate and I want to know its correct InChI, how to do this? The reason I ask is because when I go to different databases I get different results: ChEBI: $...
8
votes
2answers
123 views

SMILES vs. Graph representation in deep learning

I have been reading papers on machine learning and deep learning methods for learning molecular space and generating molecules. These methods use different representations of the molecules. The most ...
8
votes
1answer
801 views

What is kekulization (in RDKit)?

It's been a while since I've studied chemistry. Now, I am reading the documentation of RDKit. At a certain point, the term "kekulization" is mentioned. What is kekulization (in RDKit, if this is not a ...
7
votes
5answers
4k views

Is there a database on chemical reactions, similar to NIST, but far more complete?

The only thing I'm interested in is to be able to search all reactions involving that compound in the database. Equilibrium constant, reaction rate and energy of activation would all be very welcome, ...
7
votes
2answers
3k views

Extract all structures of Gaussian 09 molecular dynamics calculation using babel?

Is there a way to easily extract all the structures and energies from an ADMP calculation done in Gaussian 09? GaussView can plot them but not export them in a useful way and babel just gives me the ...
7
votes
2answers
221 views

Substructure search with RDKit

I'm trying to search for substructures with RDKit. I would like to search for structure 1 as substructure in other structures. I don't understand why it doesn't find this structure in structures 3 ...
7
votes
1answer
342 views

converting SMILES (or .mol2) to SMARTS

The conversion between different chemical structure formats, e.g. from .mol2 to .xyz, by openbabel may tied to conditions to be met. One example of such a filter is to allow such a conversion only ...
6
votes
3answers
186 views

How to index molecules in computer programs?

Is there a standard way how can the index over a molecular structure be kept in the computer? A molecule is a graph, where nodes have labels (chemical element type), and edges are chemical bonds. ...
6
votes
3answers
502 views

How to calculate hydrogen from SMILES string?

How to calculate the number of hydrogen atoms from SMILES string? For example, SMILES String: C1=CC(=C(C=C1C(CN)O)O)O The known result is C8H11NO3
6
votes
0answers
166 views

OpenBabel: how to get correct SMILES from Gaussian output?

I would like to get the molecular structure as SMILES from Gaussian output files. OpenBabel seems to be the tool made for such tasks. However, the structure is not always correct. One example: ...
5
votes
2answers
590 views

Software for compound database creation\enumeration

The only program I have found is Plexus Suite from chemaxon. (I asked for trial, but no answer to me yet). The task is: create variation of compounds, where is scaffold and different substituents: ...
5
votes
1answer
3k views

Internal (Z-Matrix) to Cartesian coordinates conversion

Is there any way to convert from Internal to Cartesian coordinates using simple formulas? I have studied and implemented: INTERNAL TO CARTESIAN by Jack D. Kunitz. But somehow the x, y and z values ...
5
votes
1answer
443 views

Generating mol files from a molecular structure image?

I have a question regarding mol files.For example I have this molecule- The mol file for this is- ...
5
votes
3answers
233 views

What is the best way to convert SMILES strings to file names?

I would like to convert SMILES strings into file names. There are many characters to avoid in file names, i.e. \/:*?"<>| or maybe even ...
5
votes
2answers
208 views

Consistent atom names PDB

Lets say you have two times the same molecule in PDB format. PDB1: ...
5
votes
1answer
112 views

What are the disadvantages of using the InChI format?

What are the disadvantages (if any) in producing and using the InChI format of chemical compound representation in chemoinformatics? Are there any particular problem one can face when using InChI?
5
votes
2answers
85 views

Freely available software for generating 3D coordinates of molecules

As part of some research I am doing, I want to do a head-to-head comparison of software for generating 3D atomic coordinates for molecules. Is there a list anywhere of chemical software that does this?...
5
votes
1answer
152 views

How can I recognize aromatic rings in a connection table?

Given a connection table (that is, a list of atoms, their connectivities/bonds, and the type of bonds), how can I detect the presence of an aromatic ring? For reference, the aromatic rings in the ...
5
votes
1answer
251 views

Search by CAS Registry name to obtain trackable accession: ie InChi?

I'm updating a database and trying to move from CAS Registry names to InChiKeys. I have about ~800 compounds to track. Is there a way to do this mappings programatically? I'm looking for a web service ...
5
votes
2answers
633 views

What is the correct regular expression for InChI?

When I look for a regular expression for InChI, I succeed on EBI's MIRIAM Registery website: ...
5
votes
1answer
146 views

Algorithm used by PubChem to determine the 2D layout assignment for Compound entries?

The PubChem database provides 2D structures for entries in its Compounds database: ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/ (ftp link to download examples) On the page linked below, under the "...
5
votes
1answer
69 views

Change inchikey directly

Preamble: Now, I am aware that directly editing the inchikey is, generally speaking, a bad idea, but... Can I just change the 2nd block of an inchikey to "UHFFFAOY" to get the correct main-layer-...
5
votes
1answer
95 views

Finding vendor information programmatically

I have a large collection of structures (>10,000) that I've gathered from literature searches and I would like to find out which of those can be obtained from vendors. I know that eMolecules and ...
5
votes
0answers
219 views

Pseudo 3D skeletal structure style which emphasizes geometry

If one searches and navigates to a wiki page for, say, dichlorodifluoromethane one sees the 2D skeletal structure of the compound as below This representation appears to be of a particular style that ...
4
votes
5answers
596 views

Free API to view 2D representation of Molecules

I'm looking for a free API that can accept a SMILE and produce the 2D structure of a molecule. I would like to include this in a web page. I have collection of SMILES and would like to have the 2D ...
4
votes
2answers
2k views

How to determine the Bravais lattice and atom basis vectors from a CIF file?

Say I have a CIF file describing some material in terms of its symmetry space group, lattice parameters and in-cell atom positions. A simple example might be, ...
4
votes
2answers
85 views

What is maximum energy level of molecules?

I have been reading about the relation of molecular graph spectrum, that is, the set of eigenvalues of the Laplacian matrix of the molecular graph, and molecular properties. Recently, I came across a ...
4
votes
1answer
50 views

Red Squares in RDKit?

I'm newish to RDKit and couldn't find an answer to this online. The following is a minimal representation of how I drew a molecule ...
4
votes
2answers
526 views

Finding all Chemical Reactions Given Products and Reactants

Suppose only a set of chemical formulas is given. How can you find all mathematically possible chemical equations whose educts and products are only from this set? Take e.g. the set $\{ \ce{C, H2, O2,...
4
votes
2answers
1k views

How do I make a ZMAT or XYZ file from scratch?

From a structure representation like the one below for Bacteriochlorophyll A, how do I make the ZMAT or XYZ file? The closest similar question asked here was about converting a PDB entry into XYZ, but ...